-
Opening URLs from Jalview
-Both the applet and the desktop application are able to open URLs as
-'popups' in your web browser.
-Double-clicking on the ID of a sequence will open the first URL that can
-be generated from its sequence ID. This is often the SRS site, but you
-can easily configure your own sequence URL links.
Other links for a sequence either derived from any other -configured URL links, or imported from the sequence's annotation, are -accessed by right clicking to open the sequence pop-up menu, and -selecting from the Links submenu.
-Configuring URL Links
-
URL links are defined in the "Connections" tab of the Jalview desktop preferences, or
-specified as applet
-parameters.
-By default the item "SRS" is added to this link menu. This
-link will show a web page in your default browser with the selected
-sequence id as part of the URL.
-In the preferences dialog box, click new to add a new
-link, and edit to modify an existing link, or delete
-to remove it.
-You can name the link, this will be displayed on a new menu item under
-the "Link" menu when you right click on a sequence id.
-The URL string must contain a token that can be replaced with a sequence
-ID. The simplest token is "$SEQUENCE_ID$", which will be
-replaced by the chosen sequence id when you click on it.
eg.
-UniRef100 =
-http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
-Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$
-
-Links will also be made for any database cross references associated
-with the sequence where the database name exactly matches a URL link
-name. In this case, the $SEQUENCE_ID$ string will be replaced with the
-accession string for the database cross-reference, rather than the
-sequence ID for the sequence (since Jalview 2.4).
Regular Expression Substitution
-A url may contain a string of the form $SEQUENCE_ID=/regular
-expression/=$. In this case, the regular expression will be applied to
-the full sequence ID string and the resulting match will be inserted
-into the URL. Groups of parentheses can be used to specify which regions
-of the regular expression will be used to generate the URL:
-
+
+ Opening URLs from Jalview
Both the applet
+ and the desktop application are able to open URLs as 'popups' in
+ your web browser.
Double-clicking on the ID of a sequence
+ will open the URL designated for 'popups' in the "Connections" tab of the Jalview desktop
+ preferences.
+ This is by default the EMBL-EBI site, but you can easily configure your own sequence URL links.
+
+ Other links for a sequence either derived from any other configured + URL links, or imported from the sequence's annotation, are accessed + by right clicking to open the sequence pop-up menu, and selecting + from the Links submenu. +
+
+ Configuring URL Links
URL
+ links are defined in the "Connections" tab of the Jalview desktop
+ preferences, or specified as applet
+ parameters.
+ By default, the list of available links in the preferences dialog box
+ contains the item "EMBL-EBI Search",
+ which is set as the URL which opens on double-clicking on a sequence ID, and as a
+ menu item in the Links menu. This link will show a web page in your default
+ browser with the selected sequence id as part of the URL.
+
+ Also by default, the list of available links contains persistent URLs for many common
+ bioinformatics databases. These links are downloaded by Jalview from
+ the identifiers.org website, and the names and URLs are not user editable.
+
+ The list of links is sortable, by clicking on the headers of the table. The list
+ can be filtered using the free text search box below the table, or the
+ "Custom Only" button, which displays only user-defined links.
+
+ In the preferences dialog box, the links which appear in the Links menu
+ can be configured by selecting or deselecting links in the "In Menu"
+ column. The names of selected links will be displayed
+ on new menu items under the "Link" menu when you right
+ click on a sequence id.
+ You can configure which link is used when double-clicking on a sequence
+ by selecting or deselecting links in the "On Click" column. Exactly one
+ link must be configured for double-clicking. Since the link uses the sequence id
+ to construct the URL to open, the selected link must contain the
+ "$SEQUENCE_ID$" token (see below for details of the "$SEQUENCE_ID$"
+ and other tokens).
+ Additionally you can click new to add a + new link, and edit to modify an existing link, or delete + to remove it. Only URLs entered by the user (or the default EMBL-EBI link) may + be edited or deleted. When adding or editing a link, the URL string must contain a + token that can be replaced with a sequence ID or DB accession ID. The simplest token is + "$SEQUENCE_ID$", which will be replaced by the chosen + sequence id when you click on it. +
+
+ eg.
UniRef100 =
+ http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
+ Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$
+ Links will also be made for any database cross references associated
+ with the sequence where the database name exactly matches a URL link
+ name. In this case, the $DB_ACCESSION$ string will be replaced with
+ the accession string for the database cross-reference, rather than
+ the sequence ID for the sequence (since Jalview 2.10.1).
+
+ Regular Expression Substitution
A url may
+ contain a string of the form $SEQUENCE_ID=/regular
+ expression/=$ or $DB_ACCESSION=/regular expression/=$.
+ In this case, the regular expression will be
+ applied to the full sequence ID or DB accession ID string and the resulting match will
+ be inserted into the URL. Groups of parentheses can be used to
+ specify which regions of the regular expression will be used to
+ generate the URL:
+